Val Piora Wheatear: Untitled

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library(GeoPressureR)
library(leaflet)
library(leaflet.extras)
library(raster)
library(dplyr)
library(ggplot2)
library(kableExtra)
library(plotly)
library(GeoLocTools)
setupGeolocation()
knitr::opts_chunk$set(echo = FALSE)
load(paste0("../data/1_pressure/", params$gdl_id, "_pressure_prob.Rdata"))
load(paste0("../data/2_light/", params$gdl_id, "_light_prob.Rdata"))
load(paste0("../data/3_static/", params$gdl_id, "_static_prob.Rdata"))
load(paste0("../data/4_basic_graph/", params$gdl_id, "_basic_graph.Rdata"))
load(paste0("../data/5_wind_graph/", params$gdl_id, "_wind_graph.Rdata"))
col <- rep(RColorBrewer::brewer.pal(8, "Dark2"), times = ceiling(max(pam$sta$sta_id) / 8))

Settings used

All the results produced here are generated with (1) the raw geolocator data, (2) the labeled files of pressure and light and (3) the parameters listed below.

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kable(gpr) %>% scroll_box(width = "100%")

gdl_id	keep	crop_start	crop_end	thr_dur	extent_N	extent_W	extent_S	extent_E	map_scale	map_max_sample	map_margin	prob_map_s	prob_map_s_calib	prob_map_thr	shift_k	kernel_adjust	calib_lon	calib_lat	calib_1_start	calib_1_end	calib_2_start	calib_2_end	calib_2_lon	calib_2_lat	prob_light_w	thr_prob_percentile	thr_gs	thr_as	RingNo	scientific_name	common_name	mass	wing_span	Color	sta_id_winter
26HS	9	2020-07-07	2021-06-23	0	51	-18	5	16	4	300	30	1	1.3	0.9	0	1.4	8.711702	46.55361	2020-07-07	2020-09-17	2021-05-13	2021-06-23	NA	NA	0.09	0.95	120	100	N643031	Oenanthe oenanthe	Northern wheatear	NA	NA	#00CC96	17

Pressure timeserie

The labeling of pressure data is illustrated with this figure. The black dots indicates the pressure datapoint not considered in the matching. Each stationary period is illustrated by a different colored line.

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pressure_na <- pam$pressure %>%
  mutate(obs = ifelse(isoutlier | sta_id == 0, NA, obs))
p <- ggplot() +
  geom_line(data = pam$pressure, aes(x = date, y = obs), colour = "grey") +
  # geom_point(data = subset(pam$pressure, isoutlier), aes(x = date, y = obs), colour = "black") +
  # geom_line(data = pressure_na, aes(x = date, y = obs, color = factor(sta_id)), size = 0.5) +
  geom_line(data = do.call("rbind", shortest_path_timeserie) %>% filter(sta_id > 0), aes(x = date, y = pressure0, col = factor(sta_id))) +
  theme_bw() +
  scale_colour_manual(values = col) +
  scale_y_continuous(name = "Pressure(hPa)")

ggplotly(p, dynamicTicks = T) %>% layout(showlegend = F)

Pressure calibration

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pressure_ts_bind <- do.call("rbind", shortest_path_timeserie) %>%
  filter(!is.na(sta_id))

pam$pressure %>%
  left_join(pressure_ts_bind %>% dplyr::select(c("date", "pressure0")), by = "date") %>%
  mutate(diff = ifelse(is.na(pressure0), 0, obs - pressure0)) %>%
  filter(sta_id > 0 & !isoutlier) %>%
  group_by(sta_id) %>%
  mutate(sta_id = paste0(sta_id, " (SD=", round(sd(diff), 2), " ; N=", n(), ")")) %>%
  ggplot(aes(x = diff)) +
  geom_histogram(aes(y = (..count..) / tapply(..count.., ..PANEL.., sum)[..PANEL..]), binwidth = .2) +
  facet_wrap(~sta_id) +
  scale_x_continuous(name = "Pressure Geolocator - best match ERA5 (hPa)") +
  scale_y_continuous(name = "Normalized histogram")

Light

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raw_geolight <- pam$light %>%
  transmute(
    Date = date,
    Light = obs
  )
lightImage(tagdata = raw_geolight, offset = 0)
tsimagePoints(twl$twilight,
  offset = 0, pch = 16, cex = 1.2,
  col = ifelse(twl$deleted, "grey20", ifelse(twl$rise, "firebrick", "cornflowerblue"))
)
abline(v = gpr$calib_2_start, lty = 1, col = "firebrick", lwd = 1.5)
abline(v = gpr$calib_1_start, lty = 1, col = "firebrick", lwd = 1.5)
abline(v = gpr$calib_2_end, lty = 2, col = "firebrick", lwd = 1.5)
abline(v = gpr$calib_1_end, lty = 2, col = "firebrick", lwd = 1.5)

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hist(z, freq = F)
lines(fit_z, col = "red")

The probability map resulting from light data alone can be seen below.

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li_s <- list()
l <- leaflet(width = "100%") %>%
  addProviderTiles(providers$Stamen.TerrainBackground) %>%
  addFullscreenControl()
for (i_r in seq_len(length(light_prob))) {
  i_s <- metadata(light_prob[[i_r]])$sta_id
  info <- pam$sta[pam$sta$sta_id == i_s, ]
  info_str <- paste0(i_s, " | ", info$start, "->", info$end)
  li_s <- append(li_s, info_str)
  l <- l %>% addRasterImage(light_prob[[i_r]], opacity = 0.8, colors = "OrRd", group = info_str)
}
l %>%
  addCircles(lng = gpr$calib_lon, lat = gpr$calib_lat, color = "black", opacity = 1) %>%
  addLayersControl(
    overlayGroups = li_s,
    options = layersControlOptions(collapsed = FALSE)
  ) %>%
  hideGroup(tail(li_s, length(li_s) - 1))

Light vs Pressure

We can compare light and pressure location at long stationary stopover (>5 days). By assuming the best match of the pressure to be the truth, we can plot the histogram of the zenith angle and compare to the fit of kernel density at the calibration site.

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 raw_geolight <- pam$light %>%
    transmute(
      Date = date,
      Light = obs
    )
 dur <- unlist(lapply(pressure_prob, function(x) difftime(metadata(x)$temporal_extent[2],metadata(x)$temporal_extent[1], units = "days" )))
  long_id <- which(dur>5)

  par(mfrow = c(2, 3))
  for (i_s in long_id){
    twl_fl <- twl %>%
      filter(!deleted) %>%
      filter(twilight>shortest_path_timeserie[[i_s]]$date[1] & twilight<tail(shortest_path_timeserie[[i_s]]$date,1))
    sun <-  solar(twl_fl$twilight)
    z_i <- refracted(zenith(sun, shortest_path_timeserie[[i_s]]$lon[1], shortest_path_timeserie[[i_s]]$lat[1]))
    hist(z_i, freq = F, main = paste0("sta_id=",i_s, " | ",nrow(twl_fl),"twls"))
    lines(fit_z, col = "red")
    xlab("Zenith angle")
  }

Similarly, we can plot the line of sunrise/sunset at the best match of pressure (yellow line) and compare to the raw and labeled light data.

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  lightImage(
    tagdata = raw_geolight,
    offset = gpr$shift_k / 60 / 60
  )
  tsimagePoints(twl$twilight,
                offset = gpr$shift_k / 60 / 60, pch = 16, cex = 1.2,
                col = ifelse(twl$deleted, "grey20", ifelse(twl$rise, "firebrick", "cornflowerblue"))
  )
  for (ts in shortest_path_timeserie){
    twl_fl <- twl %>%
      filter(twilight>ts$date[1] & twilight<tail(ts$date,1))
    if (nrow(twl_fl)>0){
    tsimageDeploymentLines(twl_fl$twilight,
                           lon = ts$lon[1], ts$lat[1],
                           offset = gpr$shift_k / 60 / 60, lwd = 3,col = adjustcolor("orange", alpha.f = 0.5))
      
    }
  }

Stationay period information

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read_csv(paste0("../reports/figure_print/table_transition/transition_", params$gdl_id, ".csv")) %>% kable() %>% scroll_box(width = "100%")

…1	sta_id_s	sta_id_t	flight_duration	as_m	as_s	gs_m	gs_s	ws_m	ws_s	dist_m	dist_s	ws_m_support	ws_m_drift	start_flight	end_flight	sunrise	sunset	as_sp	gs_sp	ws_sp	dist_sp	ws_sp_support	ws_sp_drift	alt_min	alt_max	alt_mean	alt_med	alt_sumdabsdiff	alt_sumposdiff	gdl_id
1	1	2	5.0	30.68453	13.057935	34.27395	16.489093	9.773649	3.9684847	171.36977	82.44547	4.7950044	8.516581	2020-09-16 18:00:00	2020-09-16 23:00:00	2020-09-17 04:43:48	2020-09-16 18:04:51	40.475859	50.235248	9.7759244	251.17624	9.7626044	0.5101507	2145.36853	3675.8771	2878.5442	2930.5410	3490.70038	2186.46459	26HS
2	2	3	9.5	50.93235	14.697238	45.94727	13.716450	21.291360	3.2780803	436.49903	130.30628	-0.3224493	21.288919	2020-09-23 18:00:00	2020-09-24 03:30:00	2020-09-24 04:47:23	2020-09-23 17:55:34	37.655174	31.912997	24.0638840	303.17347	2.8138656	23.8988007	182.42052	4156.9358	2158.0049	1979.0038	10619.47043	4018.23933	26HS
3	3	4	0.5	33.47795	17.753396	26.88436	24.556953	17.036418	8.9409271	13.44218	12.27848	-2.0042238	16.918116	2020-09-24 18:30:00	2020-09-24 19:00:00	2020-09-25 04:48:28	2020-09-24 17:46:36	30.557938	0.000000	30.5579381	0.00000	NA	NA	161.53503	701.1886	431.3618	431.3618	539.65361	0.00000	26HS
4	4	5	2.5	37.61044	11.982804	31.08804	27.255077	40.104694	9.5319156	77.72011	68.13769	18.6616376	35.498307	2020-09-26 18:00:00	2020-09-26 20:30:00	2020-09-27 04:48:45	2020-09-26 17:43:05	28.361540	27.732780	46.8426302	69.33195	38.9243727	26.0600310	173.99063	1655.7513	856.7018	828.1485	2938.99780	1481.76063	26HS
5	5	6	3.5	37.32223	12.080094	32.74864	16.944841	25.657295	6.2779527	114.62023	59.30694	5.1577912	25.133523	2020-09-27 18:00:00	2020-09-27 21:30:00	2020-09-28 04:50:00	2020-09-27 17:39:13	36.306794	31.730380	31.2195965	111.05633	10.4520798	29.4179746	52.06013	883.7063	432.9185	357.4654	2473.09579	1330.52256	26HS
6	6	7	2.0	32.79936	15.873912	29.61778	17.650908	27.398114	7.2092817	59.23556	35.30182	9.3199336	25.764229	2020-09-28 19:30:00	2020-09-28 21:30:00	2020-09-29 04:50:05	2020-09-28 17:37:18	26.723365	29.720904	18.0493557	59.44181	8.3270203	16.0137433	248.62151	657.9249	477.8610	547.5233	861.70503	591.49222	26HS
7	7	8	3.5	27.73450	15.820647	28.36423	15.424889	8.670571	2.7852397	99.27480	53.98711	1.9479751	8.448916	2020-09-29 18:00:00	2020-09-29 21:30:00	2020-09-30 04:54:09	2020-09-29 17:34:35	28.874010	30.055443	8.0760419	105.19405	2.2432481	7.7582402	513.35069	1221.3426	850.0072	767.4263	1784.17418	816.78713	26HS
8	8	9	1.0	33.16928	13.335200	31.71603	14.648592	6.242437	2.2755773	31.71603	14.64859	-0.8722142	6.181202	2020-09-30 03:00:00	2020-09-30 04:00:00	2020-09-30 04:54:10	2020-09-29 17:37:29	24.446279	27.755064	3.7998255	27.75506	3.3716679	1.7522928	65.18733	541.2896	326.7750	373.8480	643.54391	476.10227	26HS
9	9	10	7.0	58.80838	10.475791	56.62167	10.670219	21.674121	1.5206606	396.35169	74.69154	1.9193647	21.588969	2020-09-30 19:30:00	2020-10-01 02:30:00	2020-10-01 04:53:12	2020-09-30 17:35:52	42.367252	44.055733	24.2573937	308.39013	8.3342699	22.7807176	437.86971	2016.4987	1270.0855	1331.0905	5402.50467	2970.67348	26HS
10	10	11	1.5	34.43752	15.753038	33.23832	15.090890	10.681243	2.5198230	49.85748	22.63634	0.4953949	10.669749	2020-10-01 21:30:00	2020-10-01 23:00:00	2020-10-02 04:53:00	2020-10-01 17:32:15	24.821372	23.799505	13.4161764	35.69926	2.7376564	13.1338885	832.82805	1545.4755	1191.0610	1192.9703	1397.83367	685.18619	26HS
11	11	12	2.0	30.13985	12.838914	34.97254	19.986021	30.696724	5.2308107	69.94508	39.97204	17.9706294	24.886649	2020-10-02 22:00:00	2020-10-03 00:00:00	2020-10-03 04:53:49	2020-10-02 17:29:49	29.537018	0.000000	29.5370185	0.00000	NA	NA	655.07844	1519.1441	960.1921	860.9651	1654.05146	789.98585	26HS
12	12	13	12.5	41.27070	5.672056	47.92295	7.453933	12.239815	1.4959794	599.03686	93.17416	7.7536101	9.470724	2020-10-27 17:00:00	2020-10-28 05:30:00	2020-10-28 05:19:37	2020-10-27 16:57:47	41.769203	52.223457	11.3892241	652.79321	10.6497886	4.0368837	202.51010	2142.5083	1292.6665	1287.6847	7851.49337	3702.53657	26HS
13	13	14	12.0	44.35932	15.404116	55.19306	13.754062	20.642114	4.0997116	662.31674	165.04875	13.6305318	15.501789	2020-10-28 17:30:00	2020-10-29 05:30:00	2020-10-29 05:22:39	2020-10-28 17:12:24	35.408606	46.140757	17.5462718	553.68909	12.8202468	11.9796880	384.64443	1818.8299	1040.6961	830.3677	4449.55500	2264.72563	26HS
14	14	15	12.0	41.40153	12.776006	41.96911	14.108651	8.749411	5.6342762	503.62927	169.30381	1.4757404	8.624058	2020-10-29 17:30:00	2020-10-30 05:30:00	2020-10-30 05:21:50	2020-10-29 17:23:18	39.264987	42.018904	2.8186467	504.22685	2.7582095	0.5805597	645.36691	3416.9216	2190.2800	2496.0592	10543.40377	5256.02852	26HS
15	15	16	10.5	49.93632	14.235096	54.49087	15.323178	27.080750	4.5168518	572.15410	160.89337	11.0934706	24.704290	2020-10-30 18:00:00	2020-10-31 04:30:00	2020-10-31 05:22:08	2020-10-30 17:30:05	37.715803	45.909781	31.3797516	482.05270	18.1869196	25.5719527	417.99883	3573.4794	2435.0022	2902.8339	9077.41643	4384.91392	26HS
16	16	17	8.0	29.84593	12.607196	32.80054	13.240570	14.897625	2.3041339	262.40430	105.92456	6.2046972	13.544038	2020-11-02 19:30:00	2020-11-03 03:30:00	2020-11-03 05:23:36	2020-11-02 17:36:59	33.453763	36.008410	12.6522586	288.06728	4.6868356	11.7521580	315.72103	3595.6435	1368.7433	564.5900	7044.45501	3514.51539	26HS
17	17	18	10.5	55.83339	17.374159	56.80418	18.796785	6.154717	1.6038458	596.44392	197.36624	1.2959291	6.016736	2021-04-04 19:00:00	2021-04-05 05:30:00	2021-04-05 05:21:27	2021-04-04 18:23:34	40.793946	40.251618	8.5085744	422.64199	0.3533094	8.5012358	293.51433	2634.5002	1421.5940	1277.2729	5432.05089	2820.83394	26HS
18	18	19	11.0	39.25608	16.227342	47.51058	19.182978	19.641870	4.8476025	522.61638	211.01275	11.5976103	15.852398	2021-04-05 18:30:00	2021-04-06 05:30:00	2021-04-06 05:12:07	2021-04-05 18:29:03	38.213411	51.694704	18.1790719	568.64174	14.9198675	10.3863471	492.91829	3724.6037	2020.9953	1857.0626	7873.16386	3927.77960	26HS
19	19	20	13.5	46.33745	15.001549	69.63609	16.937205	28.613224	3.9403537	940.08723	228.65226	25.2795822	13.403706	2021-04-06 18:00:00	2021-04-07 07:30:00	2021-04-07 04:52:23	2021-04-06 18:27:55	39.664784	67.301616	30.2635452	908.57181	28.7667281	9.3998681	137.20625	3513.2854	2308.1576	2692.3910	10733.86277	5194.73413	26HS
20	20	21	10.5	34.98357	9.093269	38.01874	8.527951	13.590623	3.6916577	399.19672	89.54348	5.3431479	12.496231	2021-04-07 18:30:00	2021-04-08 05:00:00	2021-04-08 04:41:07	2021-04-07 18:23:15	32.879038	41.796460	13.1206275	438.86283	10.0255353	8.4640125	148.76157	1622.8113	913.7134	868.0826	8148.23017	4347.58972	26HS
21	21	22	10.0	51.50391	17.664230	75.56629	17.081416	30.221659	5.6573888	755.66285	170.81416	26.2746795	14.932845	2021-04-21 18:30:00	2021-04-22 04:30:00	2021-04-22 04:04:04	2021-04-21 18:33:08	44.378938	68.348751	30.8041555	683.48751	26.7082980	15.3480558	-61.97558	3240.2702	2059.4978	2125.2005	13359.12280	6100.41251	26HS
22	22	23	9.5	53.26688	17.398287	49.03497	17.393884	11.766234	2.9186766	465.83219	165.24190	-3.0028410	11.376607	2021-04-22 18:30:00	2021-04-23 04:00:00	2021-04-23 03:51:01	2021-04-22 18:38:39	50.332237	38.973753	15.4473525	370.25065	-9.9523381	11.8140452	21.86227	2411.6909	1074.5335	948.4245	7983.32058	4385.07987	26HS
23	23	24	4.0	37.56674	17.981122	36.51395	17.138402	7.690773	4.0110098	146.05581	68.55361	-0.2580294	7.686444	2021-04-23 19:00:00	2021-04-23 23:00:00	2021-04-24 03:47:44	2021-04-23 18:43:28	29.203140	28.220365	11.4761655	112.88146	1.3335758	11.3984187	113.87487	3281.7947	1170.7375	697.9754	5729.53980	2466.99454	26HS
24	24	25	1.5	35.18480	16.612404	34.55237	17.146072	3.918610	2.1908423	51.82856	25.71911	-0.4160085	3.896466	2021-04-24 03:30:00	2021-04-24 05:00:00	2021-04-24 03:46:24	2021-04-23 18:47:03	34.006954	37.046369	8.6760039	55.56955	3.9306629	7.7345286	-14.21649	907.7113	624.3152	801.8829	921.92783	921.92783	26HS
25	25	26	4.0	38.81664	15.729648	37.90035	16.162300	3.278319	1.4480667	151.60141	64.64920	-0.7855770	3.182804	2021-04-24 21:00:00	2021-04-25 01:00:00	2021-04-25 03:43:32	2021-04-24 18:49:47	25.746096	21.395799	4.4903547	85.58320	-4.3213613	1.2202960	495.29911	2367.3459	1434.5726	1456.5493	3753.75959	2518.77343	26HS
26	26	27	4.5	24.74204	11.306894	23.34843	11.824345	6.486769	1.9673419	105.06795	53.20955	-0.5341048	6.464743	2021-04-25 21:00:00	2021-04-26 01:30:00	2021-04-26 03:39:44	2021-04-25 18:54:21	6.108328	8.548688	5.8193917	38.46910	4.0727721	4.1566630	1829.07190	3395.3886	2583.0125	2570.7365	2789.38135	1023.80084	26HS
27	27	28	1.0	35.96975	18.073235	36.44787	18.791590	2.112522	2.1492833	36.44787	18.79159	0.5362060	2.043339	2021-05-01 18:30:00	2021-05-01 19:30:00	2021-05-02 03:30:23	2021-05-01 19:01:05	18.804455	19.234573	0.5369916	19.23457	0.4328052	0.3178673	1878.54269	1962.8200	1934.7276	1962.8200	84.27729	84.27729	26HS
28	28	29	1.5	34.85897	16.042749	33.45574	16.402458	6.315430	3.2035445	50.18361	24.60369	-0.8365755	6.259776	2021-05-08 22:30:00	2021-05-09 00:00:00	2021-05-09 03:21:15	2021-05-08 19:12:10	26.610900	25.646065	3.8336644	38.46910	-0.6964495	3.7698728	1896.77378	2529.5073	2172.3491	2131.5576	1056.59597	632.73348	26HS
29	29	30	1.0	37.82409	15.866114	37.18734	17.159937	10.181627	3.3185174	37.18734	17.15994	0.7516248	10.153846	2021-05-10 02:30:00	2021-05-10 03:30:00	2021-05-10 03:21:45	2021-05-09 19:15:35	37.767209	38.469098	8.1555646	38.46910	1.5599883	8.0049779	1256.28306	1935.9445	1489.0692	1274.9801	698.35840	18.69700	26HS
30	30	31	1.0	32.75175	13.849711	34.35887	16.455170	8.538680	4.8896547	34.35887	16.45517	2.6305321	8.123384	2021-05-10 22:00:00	2021-05-10 23:00:00	2021-05-11 03:21:17	2021-05-10 19:19:00	21.916812	19.234573	6.6598896	19.23457	-1.7162768	6.4349455	1149.83978	1347.5789	1249.7875	1251.9440	293.37399	197.73909	26HS
31	31	32	1.0	41.60002	15.073314	39.55006	15.234224	3.218772	0.4610956	39.55006	15.23422	-1.9721119	2.543868	2021-05-12 20:30:00	2021-05-12 21:30:00	2021-05-13 03:18:25	2021-05-12 19:22:48	37.185217	33.772434	3.6980422	33.77243	-3.3827522	1.4941567	1565.99822	1921.2420	1802.8274	1921.2420	355.24376	355.24376	26HS

26HS

Settings used

Pressure timeserie

Pressure calibration

Light

Light vs Pressure

Stationay period information